Altering cellular structure by reducing the particle size and applying heat may enhance the release of polyphenols from the plant cell matrix. The released polyphenols could ameliorate the impacts of a high-fat diet. Using a pig model in a 2 × 2 cross-over trial, we tested the effects of processing on the bioaccessibility of polyphenols in the diet, using low- and high-fat diets supplemented with raw and diced or cooked and pureed black carrots. Raw diced black carrots resulted in higher average particle size in the digesta of all gastrointestinal compartments and higher total and major short chain fatty acids in the descending colon. Supplementing the diet with raw and diced carrots also increased the colonic bacterial counts but with limited effects on gut microbiome diversity. The presence of carrots did not mitigate the negative impacts of decreased plasma antioxidant capacity and high atherogenic index induced by a high-fat diet.